To answer this differently:
The HO-M6R is not really much of a move "UP" from an MN61 in output, but your new configuration is a move up in every other possible way IMO: You've tripled your runtime while the host has only gained about 25% length, and you are now operating on guilt free lumens with the recharge-ability of li-ion cells instead of burning through $6 worth of primaries every 15-20 minutes.
The reason I asked what brand of cells you were using is actually relevant, as the battery you use can have a substantial impact on the performance of a direct drive incan configuration. Ultrafires are hit and miss, if you got some good ones, then it's probably performing pretty close to what it's supposed to, but at the other end of the spectrum, it could be performing way under ideal.
If you want to see at least a noticeable difference, without going to a insta-fire-starting super mag mod with 5000 lumens, pick up a set of [3] AW IMR18650s. And also one of the new IMR-M6 bulbs. Theoretically, the HO-M6R should also work on the new IMR cells (but it will be overdriven a bit and suffer some bulb life loss) and will be brighter on them, the IMR bulb should stand out as being at least noticeably brighter than your MN61...
Oh ... one other thing I just thought of...
I've noticed, personally, that if I were to take 2 lights, of equal output, but one large, and the other very small, the small one "seems" brighter to me, it's all in my head of course, but it has to do with the concept of expectation. You've moved to a larger host size, so the expectation has risen with it to some degree, so when you didn't see a massive leap in output, it was disappointing.
Eric